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D974–D981 Nucleic Acids Research, 2015, Vol. 43, Database issue doi: 10.1093/nar/gku986
D974–D981 Nucleic Acids Research, 2015, Vol. 43, Database issue
doi: 10.1093/nar/gku986
Published online 16 October 2014
PLAZA 3.0: an access point for plant comparative
genomics
Sebastian Proost1,2,† , Michiel Van Bel3,4,† , Dries Vaneechoutte3,4 , Yves Van de Peer3,4,5 ,
Dirk Inzé3,4 , Bernd Mueller-Roeber1,2 and Klaas Vandepoele3,4,*
1
University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476
Potsdam-Golm, Germany, 2 Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476
Potsdam-Golm, Germany, 3 VIB, Department of Plant Systems Biology, Technologiepark 927, Ghent, Belgium,
4
Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, Belgium and
5
Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
Received September 03, 2014; Revised October 02, 2014; Accepted October 03, 2014
ABSTRACT
Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through
a user-friendly web interface. Structural and functional annotation, gene families, protein domains,
phylogenetic trees and detailed information about
genome organization can easily be queried and visualized. Compared with the first version released
in 2009, which featured nine organisms, the number of integrated genomes is more than four times
higher, and now covers 37 plant species. The
new species provide a wider phylogenetic range
as well as a more in-depth sampling of specific
clades, and genomes of additional crop species are
present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and
PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from wellcharacterized plant genomes to other species. The
additional data and new features make PLAZA 3.0
(http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting
to explore genome information to study different aspects of plant biology, both in model and non-model
organisms.
INTRODUCTION
Since the introduction of next generation sequencing technologies, the price for sequencing a new genome has
* To
†
dropped considerably. While in the past almost exclusively
genomes from model organisms were sequenced, the decrease in costs has allowed numerous other plant species
with agricultural, economic, environmental or evolutionary
importance to be sequenced more recently (1). As sequencing genomic DNA has become accessible to a wide range of
researchers, many challenges related to the subsequent data
analysis remain, especially for species with large genomes
or lacking resources to facilitate genome analysis. The extraction of biological knowledge from a genome sequence,
through the detection of similarities and differences with
genomes of closely or more distantly related species, is an
important concept. By using such comparative approaches,
(i) knowledge can be transferred from model to non-model
organisms (2), (ii) insights can be gained in the evolution
of specific genes or entire metabolic and signaling pathways
(3), (iii) genes of importance for niche-specific plant adaptations can be identified (4) and (iv) large-scale genomic
events, such as whole-genome duplications (WGDs), can
be unveiled (5). As the number of potential pairwise comparisons grows superlinearly with the number of available
genomes, such comparative analyses require considerable
computational resources. Furthermore, the increase in data
poses challenges for efficient storage and retrieval of data, as
well as the visualization of data in an accessible and humaninterpretable way. Therefore, integrating genomic data from
multiple species to generate new biological insights through
comparative genomics remains important and challenging.
To overcome these issues, several online comparative genomics platforms are available, each focusing on a specific
set of organisms and features. Genome browsers give a detailed representation of the genomic sequence and associated features such as annotated genes, RNA-seq reads,
chromatin modifications, etc. (6–8). While such platforms
offer a detailed view of a single genome, comparative information is often limited and difficult to interpret in a
whom correspondence should be addressed. Tel: + 32 9 3313822; Fax: + 32 9 33 13 809; Email: [email protected]
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
C The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which
permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Nucleic Acids Research, 2015, Vol. 43, Database issue D975
multispecies context. Platforms focusing on gene families
rely on grouping homologous (derived from a common ancestor) genes (9) and within a family detailed phylogenetic
reconstructions are possible (10). Less common are tools
that look at genes in their genomic context to study crossspecies genome evolution and WGDs (11). Finally, comprehensive platforms were created (12–16) which, in contrast
to genome browsers, integrate numerous types of information (e.g. gene families, phylogenetic trees and genomic homology) along with structural and functional annotation,
providing a versatile starting point for numerous types of
analyses, going from simple sequence retrieval over exploring genomic variation to tracing the effects of large-scale
duplications.
In this manuscript, we present version 3.0 of PLAZA
(http://bioinformatics.psb.ugent.be/plaza/), an online resource that offers comparative genomics data for 37 plant
species (Supplementary Table S1) and allows users to
browse the annotated genomes, gene families and phylogenetic trees. Furthermore, functional annotation has been
transferred from model to non-model organisms using a
novel approach, enabling the identification of specific genes
or pathways across organisms. Genome organization can be
explored through different visualization tools based on gene
collinearity or synteny information. The PLAZA Workbench makes it possible for users to analyze multiple genes,
stored in an experiment, efficiently, while bulk downloads
are available for expert users to perform customized largescale analyses.
OVERVIEW AND ACCESS
PLAZA 3.0 has been divided into a monocot- and dicotcentric section containing 31 and 16 species, respectively.
This allows the total number of species included in one platform to remain small enough to perform fast searches, load
pages quickly and provide responsive visualizations. Both
databases contain 10 shared organisms, which either serve
as reference species to link between both sections or as outgroups. For each of the included species, the genome sequence and structural annotation has been included along
with functional annotation such as Gene Ontology (GO)
(17), MapMan (18) and InterPro protein domains (19).
While PLAZA can simply act as a browser for such data,
the true power of the platform emerges from additional data
types generated on top of the original genome information.
For instance, homologous genes are grouped together into
gene families using BLAST (20) and TribeMCL (21), while
subfamilies are identified using BLAST and OrthoMCL
(22). For each (sub-)family, multiple sequence alignments
are generated and stored that help to unveil conserved
protein domains. Pre-computed approximately-maximumlikelihood phylogenetic trees generated using FastTree (23)
allow users to explore orthologous and paralogous relations
between genes in detail. Based on the phylogenetic trees and
(sub-)families, high-quality functional annotations with experimental support from different model organisms (Arabidopsis thaliana, Solanum lycopersicum and Oryza sativa)
are transferred to other species lacking functional annotation. Genome evolution can be visualized and studied
through remaining collinear regions (regions with con-
served gene content and order), which were pre-computed
using i-ADHoRe 3.0 (24) and stored in the database.
On the PLAZA portal each data type has its own page,
with an intuitive and consistent layout. The top of the page
highlights the most general information, with more specific
and detailed information further down the page. Numerous
hyperlinks are present to allow users to go from one type of
data to another (e.g. from a gene to its family or orthologs,
or from a gene family to a phylogenetic tree). Every page
also has its own toolbox, which provides links to additional
analyses and detailed visualizations (Figure 1).
Expert users can download all sequences, gene families,
orthology information and functional annotation data in
bulk from an FTP server, while the PLAZA Workbench enables the efficient retrieval of sequence or functional information for a set of genes. The latter also allows performing
additional analyses, such as GO enrichment, which can be
used to unravel overrepresented GO categories in a set of
genes for any plant species present in the system.
NEW FEATURES OF PLAZA 3.0
New species
Currently more than 55 sequenced plant genomes have been
released (25), but their quality differs considerably between
model organisms that have nearly completed sequences and
other species which, so far, were sequenced at low coverage only. The latter are often presented as a collection of
small contigs that cannot be assembled into larger scaffolds or ordered into linkage groups or chromosomes. While
these low-coverage genomes can be of considerable value
in specific studies, the fragmented nature of their sequences
results in many partial gene models lacking start or stop
codons. A recurring issue with such models is that they hinder the generation of multiple sequence alignments and thus
can impair the construction of reliable phylogenetic trees.
To avoid such complications, assembly statistics accompanying manuscripts from publically available plant genomes
were carefully examined. All genomes that did not meet our
quality requirements, based on the N50 number (>500 kb),
were excluded. Additionally, in some cases where genomes
from closely related species, for instance of the same genus,
were available, only the sequence with the highest quality was retained. An overview of the number of genes and
species included in the different PLAZA versions is available in Figure 2 and Supplementary Table S1. Note that
previous PLAZA releases (14,15,26) will remain available
to the scientific community.
PLAZA 3.0––Dicots. The majority of novel genomes can
be found in the dicots section, with in total 13 new species.
Several genomes of plants with economical and agricultural
importance are now present in PLAZA, including Gossypium raimondii (cotton) (27), Eucalyptus grandis (eucalyptus)
(28), Solanum lycopersicum (tomato) (29), Solanum tuberosum (potato) (30), Beta vulgaris (sugar beet) (31), Prunus
persica (peach) (32), Citrus sinensis (sweet orange) (33), Cucumis melo (melon) (34) and Citrullus lanatus (watermelon)
(35). In addition to Arabidopsis thaliana (36) and Arabidopsis lyrata (37), which were already included in PLAZA,
D976 Nucleic Acids Research, 2015, Vol. 43, Database issue
Figure 1. Gene page in PLAZA 3.0. From top to bottom, (A) the header with the menu and search functions, (B) the general information (links to the gene
family, alternative gene names or identifiers) and Descriptions for gene AT1G01720, (C) the toolbox that allows different actions to be performed, (D)
tabs with detailed functional information and (E) the footer with links to general information. A similar layout is consistently used on all pages describing
different data types.
Nucleic Acids Research, 2015, Vol. 43, Database issue D977
Figure 2. Overview of the number of genes and genomes in the different
PLAZA versions. The bar chart (values on the left-axis) indicates the number of genes present in the different PLAZA versions. The superimposed
line charts (percentages on the right-axis) denote the percentage of genes
present in a gene family or having GO functional annotation. For each version, the number of integrated genomes is shown in parenthesis. Note that
there are 10 shared species in PLAZA 3.0 dicots and monocots (Supplementary Table S1).
three new Brassicaceae species (Capsella rubella (38), Brassica rapa (39) and Thelungiella parvula (40)) are now included. Having a large sample of closely related species allows evolutionary biologists to study genomic adaptations
to specific niches and how evolution has altered genes and
gene families in a recent evolutionary timeframe. An additional distant outgroup species, Amborella trichopoda (41),
was also included. Amborella is the last remaining member of the Amborellaceae, a sister clade to all other angiosperms, offering unique opportunities to study the diversification of flowering plants and their specific adaptations
at the genomic level.
PLAZA 3.0 ––Monocots. New genomes present in the
monocot section of PLAZA 3.0 are Musa acuminata (banana) (42), Setaria italica (foxtail millet) (43) and Hordeum
vulgare (barley) (44). All cereals from previous versions remained, though the Oryza sativa ssp. japonica (rice) genome
was updated to release 7 of MSU Rice Gene Models (45).
Improved functional annotation
In the previous versions of PLAZA, GO was used to assign Cellular Components, Molecular Functions and Biological Processes to genes, and InterPro domains (19) were
included to indicate the functional regions of encoded proteins. Both these types remain in PLAZA 3.0, but in addition MapMan (18) has been included as an additional ontology to describe gene functions. MapMan was initially designed for Arabidopsis thaliana, but has recently been applied to other plants as well. Transcription factor families
are also easier to identify in PLAZA 3.0 as PlnTFDB (46)
and PlantTFDB (47) classifications have now been integrated.
As in earlier versions, experimentally confirmed GO annotation was transferred using a stringent, tree-based, orthology projection method (14). For each gene, all orthologs
(genes derived from a common ancestor through speciation,
considered to have the same function in different organisms) were identified based on a phylogenetic tree following
a strict set of rules: (i) bootstrap values of the nodes considered needed to be 0.7 or higher and (ii) to avoid including
co-orthologs from distantly related species, tree-based orthologs were limited to either dicots or monocots.
To facilitate the projection of high-quality functional annotation data over greater phylogenetic distances, two new
methods were implemented (see Supplementary Method
1 for details). First, the integrative orthology approach
(iOrtho), where four different methods to detect orthologs
(using a BLAST-, clustering-, tree- and collinearity-based
approach) are combined into a single prediction (15), is now
used to transfer functional annotation from species with experimental evidence (Arabidopsis, tomato and rice) to all
other species. While this allows transfer over greater evolutionary distances, the use of multiple methods assures that
GO terms are only assigned to genes that are confirmed by
multiple orthology inference approaches, avoiding potential overprediction. Second, we included a method based on
homologous gene families, where enriched functional terms
(i.e. GO terms that occur in a family significantly more often than in the whole database and cover at least 50% of
the family members having primary GO annotations) are
assigned to all other family members lacking this term.
Figure 3 illustrates the fraction of genes that have a GO
Biological Process label provided by the GO consortium,
UniProtKB/Swiss-Prot or found using InterProScan (primary source, blue), found using PLAZA 3.0’s GO projection (green) or that lack an annotation (gray). While the
amount of primary annotation is similar to Gramene (release 41) (16) and PLAZA 2.5, the new GO projection is able
to assign a Biological Process to considerably more genes.
Especially for Zea mays (corn), there is a large improvement
as the current method allows information to be transferred
over large phylogenetic distances (i.e. from dicots to monocots).
On a gene page, the different sources of functional annotation are displayed and in cases where the annotation was
transferred from another gene, the origin and projection
method (homology-based, iORTHO or tree-based orthology) used are shown (Supplementary Figure S1). Users have
the option to only consider primary labels (from the GO
consortium, UniProtKB/Swiss-Prot and InterProScan), to
additionally include orthology-based projected terms, or to
take all GO annotations into account (primary, orthologybased and homology-based projection).
For the best annotated species (e.g. Arabidopsis thaliana),
well-curated genes come with short descriptions provided
by expert annotators. For species with less extensive annotation, such easily interpretable descriptions are rare or lacking completely. Therefore, AnnoMine was used to generate
text descriptions (Supplementary Method 2). This tool performed, for all genes, sequence similarity searches against
the UniProtKB/Swiss-Prot (48) database, which contain
curated high-quality gene descriptions. Gene descriptions
from BLAST hits, weighted by the BLASTP E-value, were
processed by an integrative text-mining algorithm that,
based on statistically overrepresented co-occurrences of
words, assigned a description to the gene.
D978 Nucleic Acids Research, 2015, Vol. 43, Database issue
Figure 3. Fractions of genes in Gramene (release 41), PLAZA 2.5 and PLAZA 3.0 dicots with a description and a GO Biological Process annotation for
five selected species (Arabidopsis thaliana, Brassica rapa, Glycine max, Solanum lycopersicum and Zea mays). Blue indicates the fraction with a description
or primary GO label (derived from the GO consortium, UniProtKB/Swiss-Prot or InterProScan), green the fraction with a projected GO label only and
gray the fraction without description/GO.
The fraction of genes that have a description in five selected species is shown in Figure 3. For Arabidopsis thaliana
extensive annotation efforts assigned descriptions to the
majority of the genes and while these efforts have been
transferred to closely related Brassicaceae species, for more
distant species proper descriptions are often lacking. In contrast with other platforms and earlier PLAZA releases, now
a large fraction of genes have an AnnoMine gene description (63% of the dicot and monocot protein-coding genes),
including many genes from non-model plants. Although
this text-mining procedure cannot replace expert annotators, it provides a valuable functional indication in the absence of a curated description.
Genome evolution
Collinearity, defined as conservation of gene content and
order, has been used in PLAZA to determine homologous
regions between genomes and duplicated regions within
a genome. The latter are usually remnants of large-scale
duplication events and various studies have revealed that
traces of WGDs are present in all plant genomes sequenced
to date (49). However, as gene loss and rearrangements accumulate after such an event, the detection of WGDs using
collinearity becomes increasingly difficult as their ages increase (50). Therefore, in some cases, collinearity is a suboptimal measure to detect remnants of ancient duplications.
To overcome this limitation, PLAZA 3.0 now also includes
Nucleic Acids Research, 2015, Vol. 43, Database issue D979
information on syntenic duplicates, which are paralogs from
regions with conserved gene content regardless of the order (51). As such, an additional 125 266 and 55 277 genes
were found to be putatively derived from WGDs that were
not found by the default collinearity searches in the dicots and monocots versions, respectively (Supplementary
Method 3).
as the implementation of new transfer methods, PLAZA
3.0 now offers comprehensive functional annotation for all
species included.
Technical improvements
ACKNOWLEDGEMENTS
While not directly visible for users, considerable changes
have been made to build the PLAZA 3.0 platform and store
the different data types. Structural changes to the database
and the way data are stored now allow faster retrieval, also
for complex queries comprising multiple data types. The result is that, despite the increase in data, many pages on the
website load faster. For visualizations that summarize large
amounts of data (like the Skyline plot, to browse for a locus
or region collinearity in multiple species), these improvements resulted in a 2- to 3-fold speed-up.
Furthermore, third-party tools required to build PLAZA
have been updated to their latest version or replaced by
more modern alternatives. BLAST (20), used to find similarities between proteins prior to gene family delineation,
has been upgraded from version 2.2.17 to 2.2.27+, OrthoMCL 1.4 (22) was changed to version 2.0 and InterProScan (52) version 4.6 was replaced with 5.44. In previous builds, two multiple sequence alignment algorithms
were used, namely MUSCLE for the alignments shown on
the website and ClustalW for calculations of KS (the fraction of synonymous substitutions per synonymous site) values. Now MUSCLE, which offers an excellent compromise
between speed and accuracy, is used consistently. To further reduce the amount of computing power needed to build
PLAZA 3.0, FastTree 2.1.7 (23) was selected to replace
PhyML (53) for the construction of phylogenetic trees.
More noticeable for users is that all graphs, which
previously were rendered using Flash, were replaced by
Javascripts generating SVG output. This has several advantages, such as (i) devices where Flash is not available now
will be able to display these graphs and (ii) SVGs can easily be downloaded and stored for future reference or used
as high-resolution images for publications. This in combination with a new fluid grid layout (where elements can
move position if the necessary monitor width is not available, avoiding the need for horizontal scroll bars) provides
excellent support for mobile devices, which are being used
by a growing number of visitors. Finally, GenomeView (8),
which used to be a java applet started within the browser,
has been updated and is now a web-started java application
that is considerably faster than previous versions.
The authors wish to express gratitude to the members of
AG Balazadeh (University of Potsdam and Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany) for beta testing, Björn Usadel (RWTH Aachen University, Aachen, Germany) for granting the use of MapMan data and Kevin Vanneste for help with setting up OrthoMCL 2.0. S.P., M.V.B. and D.V. parsed data, performed
quality filtering and updated the pipeline to build PLAZA
3.0 and the website. S.P. and K.V. wrote the manuscript.
Y.V.d.P., D.I. and B.M.-R. played a supervisory role. All authors read and approved the manuscript.
CONCLUSION
PLAZA 3.0 offers an important update toward new publicly available plant genomes while technical improvements
result in a web-based portal that loads faster and remains
responsive despite the increase in data. A new layout provides a richer, more intuitive user experience while supporting additional devices. Furthermore, through the integration of additional functional classification systems as well
SUPPLEMENTARY DATA
Supplementary Data are available at NAR Online.
FUNDING
German Research Foundation (FOR 948) [MU 1199/14-2
to S.P. and B.M.-R.]; Ghent University [Multidisciplinary
Research Partnership ‘Bioinformatics: from nucleotides to
networks’ (Project no. 01MR0310W), Multidisciplinary
Research Partnership ‘Biotechnology for a Sustainable
Economy’ (Project no. 01MRB510W), ‘Bijzonder Onderzoeksfonds Methusalem’ (Project no. BOF08/01M00408)];
European Research Council [European Union’s Seventh
Framework Programme (FP7/2007-2013) and ERC grant
agreement (no. (339341-AMAIZE 11)]; Belgian Science
Policy Office [Interuniversity Attraction Poles Programme
(IUAP P7/29 ‘MARS’)]. Funding for open access charge:
European Research Council [European Union’s Seventh
Framework Programme (FP7/2007-2013) and ERC grant
agreement (no. (339341-AMAIZE 11)].
Conflict of interest statement. None declared.
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Supplementary Data
PLAZA 3.0: an access point for plant comparative genomics
Sebastian Proost1,2, Michiel Van Bel3,4, Dries Vaneechoutte3,4, Yves Van de Peer3,4,5, Dirk Inzé3,4, Bernd
Mueller-Roeber1,2 and Klaas Vandepoele3,4,*
1
University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20,
14476 Potsdam-Golm, Germany
2
Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
3
VIB, Department of Plant Systems Biology, Technologiepark 927, Ghent, Belgium
4
Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, Ghent,
Belgium
5
Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
* To whom correspondence should be addressed. Tel: +00 32 (0)9 3313822; Email:
[email protected]
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint
First Authors.
Supplementary Methods
Supplementary Method 1: Projection of GO annotation
The GO projection based on reconciled phylogenetic trees, as implemented in the first release of
PLAZA (1), is complemented with two new approaches in PLAZA 3.0.
The first method is based on the Integrative Orthology (iOrtho) data present in the platform. As there
are several ways to determine orthologs, each with its own advantages and drawbacks, iOrtho was
implemented as an elegant way to combine predictions from different tools (2). Here, phylogenetic
trees, ortho-groups, blast and collinearity data are taken into account to determine if two genes are
orthologs. The underlying idea is that the more methods agree, the more evidence and therefore
confidence there is that two genes are truly orthologous. For genes with experimentally validated GO
information available, the functional annotation is transferred to other genes, if at least two out of four
methods agreed these genes were orthologs. New functional annotations inferred through orthologybased projection are assigned the Inferred from Sequence Orthology (ISO) evidence code.
The second method, which projects GO information from homologous genes, is based on functional
annotation of the majority of the genes within a homologous gene family. If 50% or more family
members are associated with a certain GO term (taking only the primary non-projected data into
account), the fold enrichment (using all genes in the database as the background ratio) is calculated
along with the significance (using the hypergeometric distribution). Those GO terms found to be at least
2-fold higher in the family compared to the background and significantly enriched (p-value <= 0.05) are
then associated with all genes of the homologous gene family. New functional annotations inferred
through homology-based projection are assigned the Inferred from Electronic Annotation (IEA) evidence
code. On a gene page the user can filter the associated GO information based on primary source,
orthology- or homology-based transfer.
For three species genes with experimental support were used for orthology-based GO projection. These
include Arabidopsis thaliana (13,134 genes with experimental evidence), Oryza sativa (764 genes) and
Solanum lycopersicum (140 genes).
Per organism, an overview of the GO evidence statics can be found on the species page (e.g.
http://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_dicots/organism/view/Solanum+lycopersic
um).
Supplementary Method 2: AnnoMine, automatic generation of gene descriptions
To assign functional descriptions to genes that lacked a human-readable summary, an integrative
homology-based text-mining algorithm was used (3). This algorithm, called AnnoMine, processes
sequence header information from a BLASTP run against the UniProtKB/Swiss-Prot (UniProt release
2013_12) (4) database (E-value cutoff 0.1, retaining the top 1000 hits). To avoid assigning noninformative descriptions to new genes, hits involving hypothetical proteins (e.g. 'Uncharacterized
protein', 'PREDICTED', 'unknown', 'unnamed protein product', 'predicted protein', 'hypothetical protein')
were removed from further processing. Next, all hits per gene were weighted according to reported Evalues and subsequently pooled together to identify, based on the different gene descriptions,
subsequent words (‘tokens’) that are statistically overrepresented, compared to a background model
containing 530,173 gene descriptions from UniProtKB/Swiss-Prot. As a result, n consequent tokens (ngrams, with 1 ≤ n ≤ 30) are reported that represent a consensus functional annotation based on
homologs of the unknown gene. To calculate the statistical overrepresentation of n-grams, the opensource Java toolkit LingPipe (http://alias-i.com/lingpipe/) was applied.
Supplementary Method 3: Synteny detection
Paralogs derived from older large-scale duplications were detected with i-ADHoRe 3.0 (5) in cloud mode
(cluster_type=cloud,cloud_gap_size=10,cloud_cluster_gap=20 and cloud_filter_method=binomial_corr),
with FDR correction enabled. In this mode i-ADHoRe will determine which regions have a similar content
without the requirement of conserved order (that is necessary for the collinearity based detection). The
genomes of different species were all processed individually using the homologous gene families from
PLAZA 3.0 (generated using BLAST (6) and TribeMCL (7)).
Supplementary Tables
Dicots
Supplementary Table S1. Species included in the different PLAZA versions. Note that in PLAZA 3.0 the
platform was split into a dicot and monocot section, though with ten overlapping species. Furthermore
some algal outgroups have been removed from version 3.0. Novel species are indicated in bold.
Species
PLAZA 1
PLAZA 2
PLAZA 2.5
PLAZA 3.0
Dicots
PLAZA 3.0
Monocots
Arabidopsis thaliana
Arabidopsis lyrata
Capsella rubella
Brassica rapa
Thellungiella parvula
Carica papaya
Gossypium raimondii
Theobroma cacao
Citrus sinensis
Populus trichocarpa
Ricinus communis
Manihot esculenta
Lotus japonicus
Medicago truncatula
Glycine max
Prunus persica
Malus domestica
Fragaria vesca
Citrullus lanatus
Cucumis melo
Eucalyptus grandis
Vitis vinifera
Solanum lycopersicum
Solanum tuberosum
Beta vulgaris
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
Monocots
Oryza sative ssp. Japonica
Oryza sative ssp. Indica
Hordeum vulgare
Brachypodium distachyon
Sorghum bicolor
Zea mays
Setaria italica
Musa acuminata
Outgroups
Amborella trichopoda
Selaginella moellendorffii
Physcomitrella patens
Chlamydomonas reinhardtii
Volvox carteri
Ostreococcus lucimarinus
Ostreococcus tauri
Micromonas sp. RCC299
Total
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
9
1
1
1
1
1
1
1
23
25
1
1
1
1
1
1
31
16
Supplementary Figure S1. Example of a Gene Page in PLAZA 3.0 showing the different sources of GO
functional annotation for gene SI002G33570.
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